Magnesium in PDB 7mj0: Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp

Enzymatic activity of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp

All present enzymatic activity of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp:
2.5.1.143;

Protein crystallography data

The structure of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp, PDB code: 7mj0 was solved by S.Chatterjee, J.A.Rankin, S.Lagishetty, J.Hu, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.79 / 3.01
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.284, 121.284, 213.406, 90, 90, 90
R / Rfree (%) 23.5 / 27.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp (pdb code 7mj0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp, PDB code: 7mj0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7mj0

Go back to Magnesium Binding Sites List in 7mj0
Magnesium binding site 1 out of 2 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:24.1
occ:1.00
O A:SER223 2.5 35.8 1.0
O A:VAL191 2.6 37.2 1.0
O A:GLY188 2.7 39.1 1.0
O A:GLY224 3.7 30.1 1.0
C A:SER223 3.7 34.7 1.0
C A:VAL191 3.7 38.1 1.0
C A:GLY188 3.7 38.2 1.0
O A:LYS193 3.9 37.1 1.0
CA A:GLY224 4.0 31.6 1.0
CA A:GLY188 4.1 36.8 1.0
OD1 A:ASP192 4.2 56.5 1.0
CA A:ASP192 4.2 54.6 1.0
C A:GLY224 4.2 29.9 1.0
N A:GLY224 4.3 31.7 1.0
CG2 A:VAL195 4.3 38.5 1.0
N A:ASP192 4.4 54.0 1.0
CE B:MET242 4.4 46.4 1.0
CG2 A:VAL191 4.5 35.3 1.0
OH B:TYR238 4.5 60.9 1.0
CE1 B:TYR238 4.7 55.6 1.0
N A:LYS193 4.7 41.5 1.0
C A:ASP192 4.8 53.8 1.0
CA A:VAL191 4.8 38.6 1.0
N A:VAL191 4.8 38.4 1.0
CA A:SER223 4.9 34.7 1.0
SD B:MET242 4.9 47.8 1.0
N A:GLY189 4.9 44.3 1.0
O A:VAL187 5.0 42.9 1.0
C A:LYS193 5.0 38.0 1.0

Magnesium binding site 2 out of 2 in 7mj0

Go back to Magnesium Binding Sites List in 7mj0
Magnesium binding site 2 out of 2 in the Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Adenosine Monophosphate Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:24.1
occ:0.38
O2P A:AMP301 2.2 76.8 0.8
OD1 A:ASP151 2.6 83.3 1.0
CG A:ASP151 3.3 84.3 1.0
OD2 A:ASP151 3.3 86.8 1.0
P A:AMP301 3.4 88.6 0.8
O5' A:AMP301 3.6 79.6 0.8
NH1 A:ARG159 3.6 77.5 1.0
CA A:GLY125 3.8 48.7 1.0
O A:ALA124 3.8 55.0 1.0
O3P A:AMP301 4.0 60.0 0.8
NH2 A:ARG159 4.0 71.3 1.0
CZ A:ARG159 4.3 74.1 1.0
N A:THR126 4.4 64.5 1.0
CB A:ASP151 4.6 82.8 1.0
O1P A:AMP301 4.6 48.1 0.8
C A:GLY125 4.7 55.0 1.0
C A:ALA124 4.7 56.1 1.0
N A:GLY125 4.8 42.0 1.0
C5' A:AMP301 4.8 66.2 0.8
CA A:ASP151 4.9 78.5 1.0

Reference:

J.A.Rankin, S.Chatterjee, Z.Tariq, S.Lagishetty, B.Desguin, J.Hu, R.P.Hausinger. The Larb Carboxylase/Hydrolase Forms A Transient Cysteinyl-Pyridine Intermediate During Nickel-Pincer Nucleotide Cofactor Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34548397
DOI: 10.1073/PNAS.2106202118
Page generated: Fri Nov 5 15:20:22 2021

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